[Vcftools-help] IMPUTE2 to VCF while retaining dosage values

[Vince F. <for...@gm...>]

Hi,

Is there a tool chain to convert IMPUTE2 data (.gen and .sample files)
to VCF format, while still retaining dosage values? For example, as a
GL formatted genotype.

So far, I have come up with:

1. IMPUTE2 to PED using GTOOL
2. PED to binary PED using PLINK
3 .binaryPED to VCF using PLINKSEQ.

But GTOOL thresholds the genotypes to integers.

Thanks in advance for the help.

Vince